However, the committee also warned there would be more deaths if horses were not vaccinated.

The report also detailed the complex debate about the use of the vaccine and the decision about whether to make it mandatory for horse owners.

It recommended new workplace safety laws to limit the liability of vets and clear requirements for protective clothing.

Committee chair and Gladstone MP, Glenn Butcher, said the inquiry's 11 recommendations were about saving lives.

"Hendra virus remains a risk for horses wherever there are flying foxes — horses that get infected generally die," he said.

"If people get the virus from infected horses they will likely die too and there is no cure.

"Vaccinating against the Hendra virus remains the most effective option for preventing horse and human deaths from the virus, according to biosecurity, workplace safety and health experts.

"If people stop vaccinating their horses, we will see deaths from Hendra virus in Queensland again."

Some vets choose not to administer vaccine

The report detailed the reasoning by Australian Pesticides and Veterinary Medicines Authority (APVMA) for approving the registration of the vaccine, but also the concerns raised by horse owners in relation to side effects.

The report stated: "The Department of Agriculture and Fisheries accepts the safety and efficacy of the HeV vaccine as determined by the APVMA".

"Despite the assurances from the APVMA, the Department of Agriculture and Fisheries and others, horse owners have questioned the vaccine's efficacy and safety.

"They argue that further testing of the vaccine is warranted on a wider range of horse breeds with differing genetic backgrounds."

The report then goes onto state: "Rather than a statistical rarity, as the adverse reaction statistics provided by Zoetis and the APMVA would suggest, horse owners describe adverse events linked to the HeV vaccine as commonplace".

It also said that many veterinarians had chosen not to administer the vaccination.

Many vets have also chosen not to treat horses who have not had the vaccine.

"Depending on location and the availability of other veterinarians, owners of unvaccinated horses may be unable to find a treating veterinarian," the report said.

But it said there were difficulties associated with the reporting and interpreting of adverse reactions to vaccinations.

The parliamentary committee carried out a short survey in relation to 20 separate horse deaths since 2013 believed to be connected to a negative reaction to the vaccine.

On closer examination, four of the 20 the horse died more than a year after the vaccination and two of the deaths had not been previously reported as caused by the vaccine.

Veterinary Association considering report recommendations

In relation to the recommendation not to make the vaccine mandatory, the report said it should be "left to the discretion of equestrian event organisers to require as a condition of entry and for horse owners to decide based on risk".

But another recommendation called for the Department of Agriculture and Fisheries to "encourage vaccination" through promoting its use to "horse owners and equestrian groups".

The committee also supported the rights of veterinarians to refuse to treat unvaccinated horses.

In April, the Australian Veterinary Association (AVA) made a submission on behalf of its 9,000 members.

At the time, the spokesperson representing equine veterinarians, Dr Nathan Anthony, said veterinarians have had to consider increasingly complex risks in their decisions relating to Hendra virus.

"This is due to a range of factors including the unpredictability of the disease, the death of two vets, and the inability to insure against business interruption if a veterinary practice is quarantined following a confirmed case of Hendra," he said in April.

The AVA was contacted by the ABC for comment, but it said it must first consider the full report before detailing any response to the recommendations of the committee.

In a statement later released by the organisation, AVA said it welcomed the recommendations.

"Overall, we are pleased with the recommendations and look forward to working with the Government in implementing them," it said.

Fears of major side effects of vaccine

Concerns had been raised in the last year in relation to potential major side effects from the vaccine, including death, despite the manufacturer disputing the claims.

A group called 'Say No To Hendra' formed on social media, and now has more than 6,000 members, including horse owners, vets and an Olympic equestrian rider, Vicki Roycroft.